We'd have to develop an external assay that can ensure immune compatibility. If we're lucky, we find a finite set of molecules that lead to immune incompatibilities from person to person and make an assay that focuses on those molecules.

Constant blood surveillance is already a fact--that is, perhaps we don't need more blood. Instead, we just do the immune sequencing on the stream that's already available. Spread out over the whole population, that's a lot of information. Firmware updates, if necessary, could be handled on an as-needed basis, or more generally like flu vaccines.

I'm not sure how the giant cube-shaped space ships will be handled--that's definitely a hurdle to consider.